Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models
(2024) In STAR Protocols 5(1).- Abstract
Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/bcab0304-7be2-4a89-82dc-17ebe15204e3
- author
- Arellano-Caicedo, Carlos LU ; Beech, Jason P. LU ; Bengtsson, Martin LU ; Ohlsson, Pelle LU and Hammer, Edith C. LU
- organization
- publishing date
- 2024-03-15
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Environmental sciences, Microbiology, Microscopy
- in
- STAR Protocols
- volume
- 5
- issue
- 1
- article number
- 102784
- publisher
- Cell Press
- external identifiers
-
- pmid:38103191
- scopus:85180278168
- ISSN
- 2666-1667
- DOI
- 10.1016/j.xpro.2023.102784
- language
- English
- LU publication?
- yes
- additional info
- Funding Information: The authors acknowledge funding from the Swedish Research Council ( VR-621-2014-5912 ), the Foundation for Strategic Research (future research leader grant SSF FFL18-0089 ), and the strategic research environment BECC . We thank Sam Bengtsson Gartner, Stephanie Casey, Saleh Moradi, and Ara Fadel Hamid for their assistance with device mass fabrication, microscopy, and image analysis. Funding Information: The authors acknowledge funding from the Swedish Research Council (VR-621-2014-5912), the Foundation for Strategic Research (future research leader grant SSF FFL18-0089), and the strategic research environment BECC. We thank Sam Bengtsson Gartner, Stephanie Casey, Saleh Moradi, and Ara Fadel Hamid for their assistance with device mass fabrication, microscopy, and image analysis. E.C.H. and C.A.-C. conceived the idea, developed the protocol design, and wrote the manuscript. C.A.-C. designed and manufactured the chips, performed the experiments, and developed the data analysis. P.O. assisted in the development of the microfluidic designs, methods, data analysis, and data interpretation. M.B. developed an adjusted protocol for the mask design and manufacturing. J.P.B. developed an adjusted protocol for the masters manufacturing. All authors contributed with the exchange of ideas and reviewed the manuscript. The authors declare no competing interests. Publisher Copyright: © 2023
- id
- bcab0304-7be2-4a89-82dc-17ebe15204e3
- date added to LUP
- 2024-01-02 16:51:28
- date last changed
- 2024-04-17 16:00:22
@article{bcab0304-7be2-4a89-82dc-17ebe15204e3, abstract = {{<p>Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).<sup>1</sup></p>}}, author = {{Arellano-Caicedo, Carlos and Beech, Jason P. and Bengtsson, Martin and Ohlsson, Pelle and Hammer, Edith C.}}, issn = {{2666-1667}}, keywords = {{Environmental sciences; Microbiology; Microscopy}}, language = {{eng}}, month = {{03}}, number = {{1}}, publisher = {{Cell Press}}, series = {{STAR Protocols}}, title = {{Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models}}, url = {{http://dx.doi.org/10.1016/j.xpro.2023.102784}}, doi = {{10.1016/j.xpro.2023.102784}}, volume = {{5}}, year = {{2024}}, }